In the game, marbles roll down a twisted path toward the goal and the player must stop them by launching new marbles into the oncoming ones. The DS touchscreen is used to 'flick' the marbles from their launch point to their destination with the stylus. The marbles disappear if player matches three or more marbles of the same type; marbles of the same color are magnetically attracted to each other over any length of wide open space, and allowing for chains of disappearances to occur.

The game is over if any marble reaches a specific point, usually near the center of each level, but using the magnetic properties of the marbles can allow one to pull marbles away from this point. Bonus items attached to marbles can, for example, temporarily slow down the rate the marbles advance or cause all marbles of a color to disappear.

In addition to the main survival mode of play, the player can take part in a quest mode, where they must clear boards under certain conditions, and a puzzle mode, where a fixed arrangement of marbles around the board must be cleared using only the few marbles made available to the player.

The WiiWare version of Magnetica supports up to four players simultaneously in either co-operative or competitive multiplayer modes, in addition to the ability to use the player's own Miis in the game. Control is done by twisting the Wii Remote left or right to turn the marble cannon, and an ability to lob marbles over others has been added.

The game features the challenge and quest modes of the DS version, but omits the puzzle mode. Extensive statistics are also kept for each player.